public static MapHeader ReadFromFile(BinaryReader reader, FileInfo info, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType)
{
MapHeader Header = null;
if (info.Extension.ToLower() == ".mrc" || info.Extension.ToLower() == ".mrcs" || info.Extension.ToLower() == ".ali" || info.Extension.ToLower() == ".rec" || info.Extension.ToLower() == ".st")
{
Header = new HeaderMRC(reader);
}
else if (info.Extension.ToLower() == ".em")
{
Header = new HeaderEM(reader);
}
else if (info.Extension.ToLower() == ".tif" || info.Extension.ToLower() == ".tiff")
{
Header = new HeaderTiff(info.FullName);
}
else if (info.Extension.ToLower() == ".dat")
{
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
{
throw new Exception("File type not supported.");
}
return(Header);
}
public static MapHeader ReadFromFile(BinaryReader reader, string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, Stream stream = null)
{
MapHeader Header = null;
string Extension = Helper.PathToExtension(path).ToLower();
if (Extension == ".mrc" || Extension == ".mrcs" || Extension == ".rec" || Extension == ".st")
Header = new HeaderMRC(reader);
else if (Extension == ".em")
Header = new HeaderEM(reader);
else if (Extension == ".dm4" || Extension == ".dm3")
Header = new HeaderDM4(reader);
else if (Extension == ".tif" || Extension == ".tiff")
Header = new HeaderTiff(path, stream);
else if (Extension == ".eer")
Header = new HeaderEER(path, stream);
else if (Extension == ".dat")
{
FileInfo info = new FileInfo(path);
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
throw new Exception("File type not supported.");
return Header;
}
public static long GetHeaderSize(string path)
{
long Position;
using (BinaryReader Reader = new BinaryReader(File.OpenRead(path)))
{
HeaderMRC Header = new HeaderMRC(Reader);
Position = Reader.BaseStream.Position;
}
return(Position);
}
public static int3 GetMapDimensions(string path)
{
int3 Dims = new int3(1, 1, 1);
FileInfo Info = new FileInfo(path);
using (BinaryReader Reader = new BinaryReader(OpenWithBigBuffer(path)))
{
if (Info.Extension.ToLower() == ".mrc" || Info.Extension.ToLower() == ".mrcs")
{
HeaderMRC Header = new HeaderMRC(Reader);
Dims = Header.Dimensions;
}
else if (Info.Extension.ToLower() == ".em")
{
HeaderEM Header = new HeaderEM(Reader);
Dims = Header.Dimensions;
}
else
throw new Exception("Format not supported.");
}
return Dims;
}
public void GrabScreenshot(string path)
{
MakeCurrent();
bool IsMRC = path.ToLower().Substring(path.Length - 3) == "mrc";
Color ScreenshotBackground = IsMRC ? Colors.Black : Colors.White;
Color OldBackground = BackgroundColor;
if (IsMRC)
{
BackgroundColor = ScreenshotBackground;
Redraw();
}
Bitmap bmp = new Bitmap(GLControl.ClientSize.Width, GLControl.ClientSize.Height);
System.Drawing.Imaging.BitmapData data = bmp.LockBits(GLControl.ClientRectangle, System.Drawing.Imaging.ImageLockMode.WriteOnly, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
GL.ReadPixels(0, 0, GLControl.ClientSize.Width, GLControl.ClientSize.Height, PixelFormat.Bgr, PixelType.UnsignedByte, data.Scan0);
bmp.UnlockBits(data);
if (!IsMRC)
{
bmp.RotateFlip(RotateFlipType.RotateNoneFlipY);
using (Stream ImageStream = File.Create(path))
{
bmp.Save(ImageStream, System.Drawing.Imaging.ImageFormat.Png);
}
}
else
{
using (BinaryWriter Writer = new BinaryWriter(File.Create(path)))
{
HeaderMRC Header = new HeaderMRC
{
Dimensions = new int3(bmp.Width, bmp.Height, 1),
Mode = MRCDataType.Byte
};
Header.Write(Writer);
int Elements = bmp.Width * bmp.Height;
byte[] Data = new byte[Elements];
System.Drawing.Imaging.BitmapData BitmapData = bmp.LockBits(GLControl.ClientRectangle, System.Drawing.Imaging.ImageLockMode.ReadOnly, System.Drawing.Imaging.PixelFormat.Format32bppArgb);
unsafe
{
fixed (byte* DataPtr = Data)
{
byte* BitmapDataP = (byte*)BitmapData.Scan0;
for (int i = 0; i < Elements; i++)
DataPtr[i] = BitmapDataP[i * 4 + 1];
}
}
bmp.UnlockBits(BitmapData);
Writer.Write(Data);
}
BackgroundColor = OldBackground;
}
}
public TiltSeries(string path)
: base(path)
{
if (Angles.Length < Dimensions.Z) // In case angles and dose haven't been read and stored in .xml yet.
{
if (File.Exists(DirectoryName + RootName + ".star"))
{
Star Table = new Star(DirectoryName + RootName + ".star");
if (!Table.HasColumn("wrpDose") || !Table.HasColumn("wrpAngleTilt"))
throw new Exception("STAR file has no wrpDose or wrpTilt column.");
List<float> TempAngles = new List<float>();
List<float> TempDose = new List<float>();
for (int i = 0; i < Table.RowCount; i++)
{
TempAngles.Add(float.Parse(Table.GetRowValue(i, "wrpAngleTilt")));
TempDose.Add(float.Parse(Table.GetRowValue(i, "wrpDose")));
}
if (TempAngles.Count == 0)
throw new Exception("Metadata must contain 2 values per tilt: angle, dose.");
if (TempAngles.Count != Dimensions.Z)
throw new Exception("Metadata must contain one line for each image in tilt series.");
Angles = TempAngles.ToArray();
Dose = TempDose.ToArray();
}
else
{
HeaderMRC Header = new HeaderMRC(new BinaryReader(File.OpenRead(Path)));
if (Header.ImodTilt != null)
{
Angles = Header.ImodTilt;
Dose = new float[Angles.Length];
}
else
throw new Exception("A .meta file with angles and accumulated dose, or at least tilt angle data in the .ali's header are needed to work with tilt series.");
}
}
}
public static MapHeader ReadFromFile(BinaryReader reader, FileInfo info, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType)
{
MapHeader Header = null;
if (info.Extension.ToLower() == ".mrc" || info.Extension.ToLower() == ".mrcs" || info.Extension.ToLower() == ".ali" || info.Extension.ToLower() == ".rec" || info.Extension.ToLower() == ".st")
Header = new HeaderMRC(reader);
else if (info.Extension.ToLower() == ".em")
Header = new HeaderEM(reader);
else if (info.Extension.ToLower() == ".tif" || info.Extension.ToLower() == ".tiff")
Header = new HeaderTiff(info.FullName);
else if (info.Extension.ToLower() == ".dat")
{
long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType);
long Slices = (info.Length - headerlessOffset) / SliceElements;
int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices);
Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType);
}
else
throw new Exception("File type not supported.");
return Header;
}
public void ExportParticlesMovieOld(Star table, int size)
{
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = table.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
MapHeader OriginalHeader = MapHeader.ReadFromFile(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
/*Image OriginalStack = StageDataLoad.LoadMap(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));*/
//OriginalStack.Xray(20f);
int3 Dims = OriginalHeader.Dimensions;
int3 DimsRegion = new int3(size, size, 1);
int NParticles = RowIndices.Count / Dimensions.Z;
float PixelSize = (float)(MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5f;
float PixelDelta = (float)(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin) * 0.5f;
float PixelAngle = (float)MainWindow.Options.CTFPixelAngle / (float)(180.0 / Math.PI);
Image CTFCoords;
{
float2[] CTFCoordsData = new float2[DimsRegion.ElementsSlice()];
//Helper.ForEachElementFT(new int2(DimsRegion), (x, y, xx, yy) =>
for (int y = 0; y < DimsRegion.Y; y++)
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle));
CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / CurrentPixelSize, angle);
} //);
CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true);
//CTFCoords.RemapToFT();
}
Image CTFFreq = CTFCoords.AsReal();
Image CTFStack = new Image(new int3(size, size, NParticles * Dimensions.Z), true);
int CTFStackIndex = 0;
string[] ColumnPosX = table.GetColumn("rlnCoordinateX");
string[] ColumnPosY = table.GetColumn("rlnCoordinateY");
int3[] Origins = new int3[NParticles];
for (int i = 0; i < NParticles; i++)
Origins[i] = new int3((int)double.Parse(ColumnPosX[RowIndices[i]]) - DimsRegion.X * 2 / 2,
(int)double.Parse(ColumnPosY[RowIndices[i]]) - DimsRegion.Y * 2 / 2,
0);
int IndexOffset = RowIndices[0];
string[] ColumnOriginX = table.GetColumn("rlnOriginX");
string[] ColumnOriginY = table.GetColumn("rlnOriginY");
string[] ColumnPriorX = table.GetColumn("rlnOriginXPrior");
string[] ColumnPriorY = table.GetColumn("rlnOriginYPrior");
float2[] ShiftPriors = new float2[NParticles];
for (int i = 0; i < NParticles; i++)
ShiftPriors[i] = new float2(float.Parse(ColumnPriorX[IndexOffset + i]),
float.Parse(ColumnPriorY[IndexOffset + i]));
float2[][] ParticleTracks = new float2[NParticles][];
for (int i = 0; i < NParticles; i++)
{
ParticleTracks[i] = new float2[Dimensions.Z];
for (int z = 0; z < Dimensions.Z; z++)
ParticleTracks[i][z] = new float2(float.Parse(ColumnOriginX[IndexOffset + z * NParticles + i]) - ShiftPriors[i].X,
float.Parse(ColumnOriginY[IndexOffset + z * NParticles + i]) - ShiftPriors[i].Y);
}
Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true);
Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Weights.Fill(1e-6f);
Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsRegion.X * 2, DimsRegion.Y * 2, NParticles));
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
/*GPU.Extract(OriginalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles.GetDevice(Intent.Write),
Dims.Slice(),
new int3(DimsRegion.X * 2, DimsRegion.Y * 2, 1),
Helper.ToInterleaved(Origins),
(uint)NParticles);*/
// Shift particles
{
float3[] Shifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[i].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[i].Y / Dims.Y, 0.85f));
float3 Coords = new float3(NormX, NormY, CoordZ);
Shifts[i] = new float3(GridMovementX.GetInterpolated(Coords) + ParticleTracks[i][z].X,
GridMovementY.GetInterpolated(Coords) + ParticleTracks[i][z].Y,
0f);
}
FrameParticles.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion));
Image FrameParticlesFT = FrameParticlesCropped.AsFFT();
FrameParticlesCropped.Dispose();
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PS.Fill(1f);
// Apply motion blur filter.
{
const int Samples = 11;
float StartZ = (z - 0.75f) * StepZ;
float StopZ = (z + 0.75f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles];
for (int p = 0; p < NParticles; p++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[p].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[p].Y / Dims.Y, 0.85f));
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = new float2(GridMovementX.GetInterpolated(Coords),
GridMovementY.GetInterpolated(Coords));
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
// Apply CTF.
if (CTF != null)
{
CTFStruct[] Structs = new CTFStruct[NParticles];
for (int p = 0; p < NParticles; p++)
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(float.Parse(ColumnPosX[RowIndices[p]]) / Dims.X,
float.Parse(ColumnPosY[RowIndices[p]]) / Dims.Y,
z * StepZ));
Structs[p] = Altered.ToStruct();
}
Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateCTF(CTFImage.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CTFCoords.ElementsSliceComplex,
Structs,
false,
(uint)NParticles);
//CTFImage.Abs();
PS.Multiply(CTFImage);
//CTFImage.WriteMRC("ctf.mrc");
CTFImage.Dispose();
}
// Apply dose weighting.
/*{
float3 NikoConst = new float3(0.245f, -1.665f, 2.81f);
// Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert!
float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize);
Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true);
GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read),
DoseImage.GetDevice(Intent.Write),
(uint)DoseImage.ElementsSliceComplex,
new[] { FrameDose },
NikoConst,
1);
PS.MultiplySlices(DoseImage);
//DoseImage.WriteMRC("dose.mrc");
DoseImage.Dispose();
}*/
// Copy custom CTF into the CTF stack
GPU.CopyDeviceToDevice(PS.GetDevice(Intent.Read),
new IntPtr((long)CTFStack.GetDevice(Intent.Write) + CTFStack.ElementsSliceReal * NParticles * z * sizeof (float)),
CTFStack.ElementsSliceReal * NParticles);
Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PSAbs.Abs();
FrameParticlesFT.Multiply(PSAbs);
AverageFT.Add(FrameParticlesFT);
Weights.Add(PSAbs);
PS.Multiply(PSAbs);
AveragePS.Add(PS);
PS.Dispose();
FrameParticlesFT.Dispose();
PSAbs.Dispose();
// Write paths to custom CTFs into the .star
for (int i = 0; i < NParticles; i++)
{
string ParticleCTFPath = (CTFStackIndex + 1).ToString("D6") + "@particlectf/" + RootName + ".mrcs";
table.SetRowValue(RowIndices[NParticles * z + i], "rlnCtfImage", ParticleCTFPath);
CTFStackIndex++;
}
}
FrameParticles.Dispose();
CTFCoords.Dispose();
CTFFreq.Dispose();
AverageFT.Divide(Weights);
AveragePS.Divide(Weights);
Weights.Dispose();
Image AverageParticles = AverageFT.AsIFFT();
AverageFT.Dispose();
GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(90f / PixelSize), true, (uint)NParticles);
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader);
AverageParticles.Dispose();
//OriginalStack.Dispose();
CTFStack.WriteMRC(DirectoryName + "particlectf/" + RootName + ".mrcs");
CTFStack.Dispose();
/*for (int i = 0; i < NParticles; i++)
{
string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
table.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath);
}*/
AveragePS.Dispose();
//table.RemoveRows(RowIndices.Skip(NParticles).ToArray());
}
public void ExportParticlesMovie(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor)
{
int CurrentDevice = GPU.GetDevice();
#region Make sure directories exist.
lock (tableIn)
{
if (!Directory.Exists(ParticleMoviesDir))
Directory.CreateDirectory(ParticleMoviesDir);
if (!Directory.Exists(ParticleCTFMoviesDir))
Directory.CreateDirectory(ParticleCTFMoviesDir);
}
#endregion
#region Get row indices for all, and individual halves
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
//RowIndices = RowIndices.Take(13).ToList();
List<int> RowIndices1 = new List<int>();
List<int> RowIndices2 = new List<int>();
for (int i = 0; i < RowIndices.Count; i++)
if (tableIn.GetRowValue(RowIndices[i], "rlnRandomSubset") == "1")
RowIndices1.Add(RowIndices[i]);
else
RowIndices2.Add(RowIndices[i]);
#endregion
if (RowIndices.Count == 0)
return;
#region Auxiliary variables
List<int> TableOutIndices = new List<int>();
int3 Dims = originalHeader.Dimensions;
Dims.Z = 36;
int3 DimsRegion = new int3(size, size, 1);
int3 DimsPadded = new int3(size * 2, size * 2, 1);
int NParticles = RowIndices.Count;
int NParticles1 = RowIndices1.Count;
int NParticles2 = RowIndices2.Count;
float PixelSize = (float)CTF.PixelSize / 1.00f;
float PixelDelta = (float)CTF.PixelSizeDelta / 1.00f;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
#endregion
#region Prepare initial coordinates and shifts
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
int3[] Origins1 = new int3[NParticles1];
int3[] Origins2 = new int3[NParticles2];
float3[] ResidualShifts1 = new float3[NParticles1];
float3[] ResidualShifts2 = new float3[NParticles2];
lock (tableIn) // Writing to the table, better be on the safe side
{
// Half1: Add translational shifts to coordinates, sans the fractional part
for (int i = 0; i < NParticles1; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices1[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices1[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins1[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts1[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateX", Origins1[i].X.ToString());
tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateY", Origins1[i].Y.ToString());
tableIn.SetRowValue(RowIndices1[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices1[i], "rlnOriginY", "0.0");
}
// Half2: Add translational shifts to coordinates, sans the fractional part
for (int i = 0; i < NParticles2; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices2[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices2[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins2[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts2[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateX", Origins2[i].X.ToString());
tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateY", Origins2[i].Y.ToString());
tableIn.SetRowValue(RowIndices2[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices2[i], "rlnOriginY", "0.0");
}
}
#endregion
#region Allocate memory for particle and PS stacks
Image ParticleStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z));
Image ParticleStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z));
Image ParticleStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z));
Image PSStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z), true);
Image PSStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z), true);
Image PSStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z), true);
Image FrameParticles1 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles1));
Image FrameParticles2 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles2));
float[][] ParticleStackData = ParticleStackAll.GetHost(Intent.Write);
float[][] ParticleStackData1 = ParticleStack1.GetHost(Intent.Write);
float[][] ParticleStackData2 = ParticleStack2.GetHost(Intent.Write);
float[][] PSStackData = PSStackAll.GetHost(Intent.Write);
float[][] PSStackData1 = PSStack1.GetHost(Intent.Write);
float[][] PSStackData2 = PSStack2.GetHost(Intent.Write);
#endregion
#region Create rows in outTable
lock (tableOut) // Creating rows in outTable, this absolutely needs to be staged sequentially
{
for (int z = 0; z < Dims.Z; z++)
{
for (int i = 0; i < NParticles; i++)
{
int Index = i < NParticles1 ? RowIndices1[i] : RowIndices2[i - NParticles1];
string OriParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
string ParticleName = (z * NParticles + i + 1).ToString("D6") + "@particlemovies/" + RootName + "_particles.mrcs";
string ParticleCTFName = (z * NParticles + i + 1).ToString("D6") + "@particlectfmovies/" + RootName + "_particlectf.mrcs";
List<string> NewRow = tableIn.GetRow(Index).Select(v => v).ToList(); // Get copy of original row.
NewRow[tableOut.GetColumnIndex("rlnOriginalParticleName")] = OriParticlePath;
NewRow[tableOut.GetColumnIndex("rlnAngleRotPrior")] = tableIn.GetRowValue(Index, "rlnAngleRot");
NewRow[tableOut.GetColumnIndex("rlnAngleTiltPrior")] = tableIn.GetRowValue(Index, "rlnAngleTilt");
NewRow[tableOut.GetColumnIndex("rlnAnglePsiPrior")] = tableIn.GetRowValue(Index, "rlnAnglePsi");
NewRow[tableOut.GetColumnIndex("rlnOriginXPrior")] = "0.0";
NewRow[tableOut.GetColumnIndex("rlnOriginYPrior")] = "0.0";
NewRow[tableOut.GetColumnIndex("rlnImageName")] = ParticleName;
NewRow[tableOut.GetColumnIndex("rlnCtfImage")] = ParticleCTFName;
NewRow[tableOut.GetColumnIndex("rlnMicrographName")] = (z + 1).ToString("D6") + "@stack/" + RootName + "_movie.mrcs";
TableOutIndices.Add(tableOut.RowCount);
tableOut.AddRow(NewRow);
}
}
}
#endregion
#region For every frame, extract particles from each half; shift, correct, and norm them
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
#region Extract, correct, and norm particles
#region Half 1
{
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles1.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins1.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles1);
// Shift particles
{
float3[] Shifts = new float3[NParticles1];
for (int i = 0; i < NParticles1; i++)
{
float3 Coords = new float3((float)Origins1[i].X / Dims.X, (float)Origins1[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts1[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles1.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles1.AsPadded(new int2(DimsRegion));
Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion),
PixelSize + PixelDelta / 2f,
PixelSize - PixelDelta / 2f,
PixelAngle,
6);
FrameParticlesCropped.Dispose();
GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read),
FrameParticlesCorrected.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / PixelSize),
true,
(uint)NParticles1);
float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read);
for (int n = 0; n < NParticles1; n++)
{
ParticleStackData[z * NParticles + n] = FrameParticlesCorrectedData[n];
ParticleStackData1[z * NParticles1 + n] = FrameParticlesCorrectedData[n];
}
//FrameParticlesCorrected.WriteMRC("intermediate_particles1.mrc");
FrameParticlesCorrected.Dispose();
}
#endregion
#region Half 2
{
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles2.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins2.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles2);
// Shift particles
{
float3[] Shifts = new float3[NParticles2];
for (int i = 0; i < NParticles2; i++)
{
float3 Coords = new float3((float)Origins2[i].X / Dims.X, (float)Origins2[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts2[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles2.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles2.AsPadded(new int2(DimsRegion));
Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion),
PixelSize + PixelDelta / 2f,
PixelSize - PixelDelta / 2f,
PixelAngle,
6);
FrameParticlesCropped.Dispose();
GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read),
FrameParticlesCorrected.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / PixelSize),
true,
(uint)NParticles2);
float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read);
for (int n = 0; n < NParticles2; n++)
{
ParticleStackData[z * NParticles + NParticles1 + n] = FrameParticlesCorrectedData[n];
ParticleStackData2[z * NParticles2 + n] = FrameParticlesCorrectedData[n];
}
//FrameParticlesCorrected.WriteMRC("intermediate_particles2.mrc");
FrameParticlesCorrected.Dispose();
}
#endregion
#endregion
#region PS Half 1
{
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true);
PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles1];
for (int p = 0; p < NParticles1; p++)
{
float NormX = (float)Origins1[p].X / Dims.X;
float NormY = (float)Origins1[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f;
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles1);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
#endregion
float[][] PSData = PS.GetHost(Intent.Read);
for (int n = 0; n < NParticles1; n++)
PSStackData[z * NParticles + n] = PSData[n];
//PS.WriteMRC("intermediate_ps1.mrc");
PS.Dispose();
}
#endregion
#region PS Half 2
{
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true);
PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles2];
for (int p = 0; p < NParticles2; p++)
{
float NormX = (float)Origins2[p].X / Dims.X;
float NormY = (float)Origins2[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f;
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles2);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
#endregion
float[][] PSData = PS.GetHost(Intent.Read);
for (int n = 0; n < NParticles2; n++)
PSStackData[z * NParticles + NParticles1 + n] = PSData[n];
//PS.WriteMRC("intermediate_ps2.mrc");
PS.Dispose();
}
#endregion
}
FrameParticles1.Dispose();
FrameParticles2.Dispose();
originalStack.FreeDevice();
#endregion
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
// Do translation and rotation BFGS per particle
{
float MaxHigh = 2.6f;
CubicGrid GridX = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridY = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridRot = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridTilt = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridPsi = new CubicGrid(new int3(NParticles1, 1, 2));
int2 DimsCropped = new int2(DimsRegion / (MaxHigh / PixelSize / 2f)) / 2 * 2;
#region Get coordinates for CTF and Fourier-space shifts
Image CTFCoords;
Image ShiftFactors;
{
float2[] CTFCoordsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y];
float2[] ShiftFactorsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y];
for (int y = 0; y < DimsCropped.Y; y++)
for (int x = 0; x < DimsCropped.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsCropped.Y / 2 + 1 ? y : y - DimsCropped.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
CTFCoordsData[y * (DimsCropped.X / 2 + 1) + x] = new float2(r / PixelSize, angle);
ShiftFactorsData[y * (DimsCropped.X / 2 + 1) + x] = new float2((float)-xx / DimsRegion.X * 2f * (float)Math.PI,
(float)-yy / DimsRegion.X * 2f * (float)Math.PI);
}
CTFCoords = new Image(CTFCoordsData, new int3(DimsCropped), true);
ShiftFactors = new Image(ShiftFactorsData, new int3(DimsCropped), true);
}
#endregion
#region Get inverse sigma2 spectrum for this micrograph from Relion's model.star
Image Sigma2Noise = new Image(new int3(DimsCropped), true);
{
int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber"));
//Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber);
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length && ir >= size / (50f / PixelSize) && ir < DimsCropped.X / 2)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir];
}
Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
Sigma2Noise.RemapToFT();
}
//Sigma2Noise.WriteMRC("d_sigma2noise.mrc");
#endregion
#region Initialize particle angles for both halves
float3[] ParticleAngles1 = new float3[NParticles1];
float3[] ParticleAngles2 = new float3[NParticles2];
for (int p = 0; p < NParticles1; p++)
ParticleAngles1[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleRot")),
float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleTilt")),
float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAnglePsi")));
for (int p = 0; p < NParticles2; p++)
ParticleAngles2[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleRot")),
float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleTilt")),
float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAnglePsi")));
#endregion
#region Prepare masks
Image Masks1, Masks2;
{
// Half 1
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolMaskFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image MasksFT = VolMaskFT.AsProjections(ParticleAngles1.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(),
new int2(DimsRegion),
MainWindow.Options.ProjectionOversample);
VolMaskFT.Dispose();
Masks1 = MasksFT.AsIFFT();
MasksFT.Dispose();
Masks1.RemapFromFT();
Parallel.ForEach(Masks1.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f;
});
}
// Half 2
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof(float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolMaskFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image MasksFT = VolMaskFT.AsProjections(ParticleAngles2.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(),
new int2(DimsRegion),
MainWindow.Options.ProjectionOversample);
VolMaskFT.Dispose();
Masks2 = MasksFT.AsIFFT();
MasksFT.Dispose();
Masks2.RemapFromFT();
Parallel.ForEach(Masks2.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f;
});
}
}
//Masks1.WriteMRC("d_masks1.mrc");
//Masks2.WriteMRC("d_masks2.mrc");
#endregion
#region Load and prepare references for both halves
Image VolRefFT1;
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.ReferencePath, new int2(1, 1), 0, typeof(float));
//GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1);
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolRefFT1 = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
VolRefFT1.FreeDevice();
Image VolRefFT2;
{
// Can't assume there is a second half, but certainly hope so
string Half2Path = MainWindow.Options.ReferencePath;
if (Half2Path.Contains("half1"))
Half2Path = Half2Path.Replace("half1", "half2");
Image Volume = StageDataLoad.LoadMap(Half2Path, new int2(1, 1), 0, typeof(float));
//GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1);
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolRefFT2 = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
VolRefFT2.FreeDevice();
#endregion
#region Prepare particles: group and resize to DimsCropped
Image ParticleStackFT1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true);
{
GPU.CreatePolishing(ParticleStack1.GetDevice(Intent.Read),
ParticleStackFT1.GetDevice(Intent.Write),
Masks1.GetDevice(Intent.Read),
new int2(DimsRegion),
DimsCropped,
NParticles1,
Dims.Z);
ParticleStack1.FreeDevice();
Masks1.Dispose();
/*Image Amps = ParticleStackFT1.AsIFFT();
Amps.RemapFromFT();
Amps.WriteMRC("d_particlestackft1.mrc");
Amps.Dispose();*/
}
Image ParticleStackFT2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true);
{
GPU.CreatePolishing(ParticleStack2.GetDevice(Intent.Read),
ParticleStackFT2.GetDevice(Intent.Write),
Masks2.GetDevice(Intent.Read),
new int2(DimsRegion),
DimsCropped,
NParticles2,
Dims.Z);
ParticleStack1.FreeDevice();
Masks2.Dispose();
/*Image Amps = ParticleStackFT2.AsIFFT();
Amps.RemapFromFT();
Amps.WriteMRC("d_particlestackft2.mrc");
Amps.Dispose();*/
}
#endregion
Image Projections1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true);
Image Projections2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true);
Image Shifts1 = new Image(new int3(NParticles1, Dims.Z / 3, 1), false, true);
float3[] Angles1 = new float3[NParticles1 * Dims.Z / 3];
CTFStruct[] CTFParams1 = new CTFStruct[NParticles1 * Dims.Z / 3];
Image Shifts2 = new Image(new int3(NParticles2, Dims.Z / 3, 1), false, true);
float3[] Angles2 = new float3[NParticles2 * Dims.Z / 3];
CTFStruct[] CTFParams2 = new CTFStruct[NParticles2 * Dims.Z / 3];
float[] BFacs =
{
-3.86f,
0.00f,
-17.60f,
-35.24f,
-57.48f,
-93.51f,
-139.57f,
-139.16f
};
#region Initialize defocus and phase shift values
float[] InitialDefoci1 = new float[NParticles1 * (Dims.Z / 3)];
float[] InitialPhaseShifts1 = new float[NParticles1 * (Dims.Z / 3)];
float[] InitialDefoci2 = new float[NParticles2 * (Dims.Z / 3)];
float[] InitialPhaseShifts2 = new float[NParticles2 * (Dims.Z / 3)];
for (int z = 0, i = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles1; p++, i++)
{
InitialDefoci1[i] = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
InitialPhaseShifts1[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
CTF Alt = CTF.GetCopy();
Alt.PixelSize = (decimal)PixelSize;
Alt.PixelSizeDelta = 0;
Alt.Defocus = (decimal)InitialDefoci1[i];
Alt.PhaseShift = (decimal)InitialPhaseShifts1[i];
//Alt.Bfactor = (decimal)BFacs[z];
CTFParams1[i] = Alt.ToStruct();
}
}
for (int z = 0, i = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles2; p++, i++)
{
InitialDefoci2[i] = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
InitialPhaseShifts2[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
CTF Alt = CTF.GetCopy();
Alt.PixelSize = (decimal)PixelSize;
Alt.PixelSizeDelta = 0;
Alt.Defocus = (decimal)InitialDefoci2[i];
Alt.PhaseShift = (decimal)InitialPhaseShifts2[i];
//Alt.Bfactor = (decimal)BFacs[z];
CTFParams2[i] = Alt.ToStruct();
}
}
#endregion
#region SetPositions lambda
Action<double[]> SetPositions = input =>
{
float BorderZ = 0.5f / (Dims.Z / 3);
GridX = new CubicGrid(new int3(NParticles, 1, 2), input.Take(NParticles * 2).Select(v => (float)v).ToArray());
GridY = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredX = GridX.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredY = GridY.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
GridRot = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridTilt = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridPsi = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredRot = GridRot.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredTilt = GridTilt.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredPsi = GridPsi.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] ShiftData1 = Shifts1.GetHost(Intent.Write)[0];
float[] ShiftData2 = Shifts2.GetHost(Intent.Write)[0];
for (int z = 0; z < Dims.Z / 3; z++)
{
// Half 1
for (int p = 0; p < NParticles1; p++)
{
int i1 = z * NParticles1 + p;
int i = z * NParticles + p;
ShiftData1[i1 * 2] = AlteredX[i];
ShiftData1[i1 * 2 + 1] = AlteredY[i];
Angles1[i1] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad);
}
// Half 2
for (int p = 0; p < NParticles2; p++)
{
int i2 = z * NParticles2 + p;
int i = z * NParticles + NParticles1 + p;
ShiftData2[i2 * 2] = AlteredX[i];
ShiftData2[i2 * 2 + 1] = AlteredY[i];
Angles2[i2] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad);
}
}
};
#endregion
#region EvalIndividuals lambda
Func<double[], bool, double[]> EvalIndividuals = (input, redoProj) =>
{
SetPositions(input);
if (redoProj)
{
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
}
/*{
Image ProjectionsAmps = Projections1.AsIFFT();
ProjectionsAmps.RemapFromFT();
ProjectionsAmps.WriteMRC("d_projectionsamps1.mrc");
ProjectionsAmps.Dispose();
}
{
Image ProjectionsAmps = Projections2.AsIFFT();
ProjectionsAmps.RemapFromFT();
ProjectionsAmps.WriteMRC("d_projectionsamps2.mrc");
ProjectionsAmps.Dispose();
}*/
float[] Diff1 = new float[NParticles1];
float[] DiffAll1 = new float[NParticles1 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams1,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts1.GetDevice(Intent.Read),
Diff1,
DiffAll1,
(uint)NParticles1,
(uint)Dims.Z / 3);
float[] Diff2 = new float[NParticles2];
float[] DiffAll2 = new float[NParticles2 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams2,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts2.GetDevice(Intent.Read),
Diff2,
DiffAll2,
(uint)NParticles2,
(uint)Dims.Z / 3);
double[] DiffBoth = new double[NParticles];
for (int p = 0; p < NParticles1; p++)
DiffBoth[p] = Diff1[p];
for (int p = 0; p < NParticles2; p++)
DiffBoth[NParticles1 + p] = Diff2[p];
return DiffBoth;
};
#endregion
Func<double[], double> Eval = input =>
{
float Result = MathHelper.Mean(EvalIndividuals(input, true).Select(v => (float)v)) * NParticles;
Debug.WriteLine(Result);
return Result;
};
Func<double[], double[]> Grad = input =>
{
SetPositions(input);
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
double[] Result = new double[input.Length];
double Step = 0.1;
int NVariables = 10; // (Shift + Euler) * 2
for (int v = 0; v < NVariables; v++)
{
double[] InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
int iv = i / NParticles;
if (iv == v)
InputPlus[i] = input[i] + Step;
else
InputPlus[i] = input[i];
}
double[] ScorePlus = EvalIndividuals(InputPlus, v >= 4);
double[] InputMinus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
int iv = i / NParticles;
if (iv == v)
InputMinus[i] = input[i] - Step;
else
InputMinus[i] = input[i];
}
double[] ScoreMinus = EvalIndividuals(InputMinus, v >= 4);
for (int i = 0; i < NParticles; i++)
Result[v * NParticles + i] = (ScorePlus[i] - ScoreMinus[i]) / (Step * 2.0);
}
return Result;
};
double[] StartParams = new double[NParticles * 2 * 5];
for (int i = 0; i < NParticles * 2; i++)
{
int p = i % NParticles;
StartParams[NParticles * 2 * 0 + i] = 0;
StartParams[NParticles * 2 * 1 + i] = 0;
if (p < NParticles1)
{
StartParams[NParticles * 2 * 2 + i] = ParticleAngles1[p].X / 1.0;
StartParams[NParticles * 2 * 3 + i] = ParticleAngles1[p].Y / 1.0;
StartParams[NParticles * 2 * 4 + i] = ParticleAngles1[p].Z / 1.0;
}
else
{
p -= NParticles1;
StartParams[NParticles * 2 * 2 + i] = ParticleAngles2[p].X / 1.0;
StartParams[NParticles * 2 * 3 + i] = ParticleAngles2[p].Y / 1.0;
StartParams[NParticles * 2 * 4 + i] = ParticleAngles2[p].Z / 1.0;
}
}
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad);
Optimizer.Epsilon = 3e-7;
Optimizer.Maximize(StartParams);
#region Calculate particle quality for high frequencies
float[] ParticleQuality = new float[NParticles * (Dims.Z / 3)];
{
Sigma2Noise.Dispose();
Sigma2Noise = new Image(new int3(DimsCropped), true);
{
int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber"));
//Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber);
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length && ir >= size / (4.0f / PixelSize) && ir < DimsCropped.X / 2)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir] / (ir * 3.14f);
}
Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
Sigma2Noise.RemapToFT();
}
//Sigma2Noise.WriteMRC("d_sigma2noiseScore.mrc");
SetPositions(StartParams);
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
float[] Diff1 = new float[NParticles1];
float[] ParticleQuality1 = new float[NParticles1 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams1,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts1.GetDevice(Intent.Read),
Diff1,
ParticleQuality1,
(uint)NParticles1,
(uint)Dims.Z / 3);
float[] Diff2 = new float[NParticles2];
float[] ParticleQuality2 = new float[NParticles2 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams2,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts2.GetDevice(Intent.Read),
Diff2,
ParticleQuality2,
(uint)NParticles2,
(uint)Dims.Z / 3);
for (int z = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles1; p++)
ParticleQuality[z * NParticles + p] = ParticleQuality1[z * NParticles1 + p];
for (int p = 0; p < NParticles2; p++)
ParticleQuality[z * NParticles + NParticles1 + p] = ParticleQuality2[z * NParticles2 + p];
}
}
#endregion
lock (tableOut) // Only changing cell values, but better be safe in case table implementation changes later
{
GridX = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Take(NParticles * 2).Select(v => (float)v).ToArray());
GridY = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredX = GridX.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredY = GridY.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
GridRot = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridTilt = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridPsi = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredRot = GridRot.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredTilt = GridTilt.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredPsi = GridPsi.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
for (int i = 0; i < TableOutIndices.Count; i++)
{
int p = i % NParticles;
int z = i / NParticles;
float Defocus = 0, PhaseShift = 0;
if (p < NParticles1)
{
Defocus = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
}
else
{
p -= NParticles1;
Defocus = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
}
tableOut.SetRowValue(TableOutIndices[i], "rlnOriginX", AlteredX[i].ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnOriginY", AlteredY[i].ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAngleRot", (-AlteredRot[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAngleTilt", (-AlteredTilt[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAnglePsi", (-AlteredPsi[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusU", ((Defocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusV", ((Defocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnPhaseShift", (PhaseShift * 180f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnCtfFigureOfMerit", (ParticleQuality[(z / 3) * NParticles + (i % NParticles)]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnMagnification", ((float)MainWindow.Options.CTFDetectorPixel * 10000f / PixelSize).ToString());
}
}
VolRefFT1.Dispose();
VolRefFT2.Dispose();
Projections1.Dispose();
Projections2.Dispose();
Sigma2Noise.Dispose();
ParticleStackFT1.Dispose();
ParticleStackFT2.Dispose();
Shifts1.Dispose();
Shifts2.Dispose();
CTFCoords.Dispose();
ShiftFactors.Dispose();
ParticleStack1.Dispose();
ParticleStack2.Dispose();
PSStack1.Dispose();
PSStack2.Dispose();
}
// Write movies to disk asynchronously, so the next micrograph can load.
Thread SaveThread = new Thread(() =>
{
GPU.SetDevice(CurrentDevice); // It's a separate thread, make sure it's using the same device
ParticleStackAll.WriteMRC(ParticleMoviesPath, ParticlesHeader);
//ParticleStackAll.WriteMRC("D:\\gala\\particlemovies\\" + RootName + "_particles.mrcs", ParticlesHeader);
ParticleStackAll.Dispose();
PSStackAll.WriteMRC(ParticleCTFMoviesPath);
//PSStackAll.WriteMRC("D:\\rado27\\particlectfmovies\\" + RootName + "_particlectf.mrcs");
PSStackAll.Dispose();
});
SaveThread.Start();
}
public void ExportParticles(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor)
{
if (!tableIn.HasColumn("rlnAutopickFigureOfMerit"))
tableIn.AddColumn("rlnAutopickFigureOfMerit");
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
int3 Dims = originalHeader.Dimensions;
int3 DimsRegion = new int3(size, size, 1);
int3 DimsPadded = new int3(size * 2, size * 2, 1);
int NParticles = RowIndices.Count;
float PixelSize = (float)CTF.PixelSize;
float PixelDelta = (float)CTF.PixelSizeDelta;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
/*Image CTFCoords;
Image CTFFreq;
{
float2[] CTFCoordsData = new float2[(DimsRegion.X / 2 + 1) * DimsRegion.Y];
float[] CTFFreqData = new float[(DimsRegion.X / 2 + 1) * DimsRegion.Y];
for (int y = 0; y < DimsRegion.Y; y++)
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle));
CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, angle);
CTFFreqData[y * (DimsRegion.X / 2 + 1) + x] = r / CurrentPixelSize;
}
CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true);
CTFFreq = new Image(CTFFreqData, DimsRegion.Slice(), true);
}*/
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
int3[] Origins = new int3[NParticles];
float3[] ResidualShifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString());
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString());
tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0");
}
Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true);
Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Weights.Fill(1e-6f);
Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles));
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles);
// Shift particles
{
float3[] Shifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float3 Coords = new float3((float)Origins[i].X / Dims.X, (float)Origins[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion));
Image FrameParticlesFT = FrameParticlesCropped.AsFFT();
FrameParticlesCropped.Dispose();
//Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
//PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
/*{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles];
for (int p = 0; p < NParticles; p++)
{
float NormX = (float)Origins[p].X / Dims.X;
float NormY = (float)Origins[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords);
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}*/
#endregion
// Apply CTF.
#region CTF weighting
/*if (CTF != null)
{
CTFStruct[] Structs = new CTFStruct[NParticles];
for (int p = 0; p < NParticles; p++)
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(Origins[p].X / Dims.X,
Origins[p].Y / Dims.Y,
z * StepZ));
Structs[p] = Altered.ToStruct();
}
Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateCTF(CTFImage.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CTFCoords.ElementsSliceComplex,
Structs,
false,
(uint)NParticles);
//CTFImage.Abs();
PS.Multiply(CTFImage);
//CTFImage.WriteMRC("ctf.mrc");
CTFImage.Dispose();
}*/
#endregion
// Apply dose.
#region Dose weighting
/*{
float3 NikoConst = new float3(0.245f, -1.665f, 2.81f);
// Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert!
float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize);
Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true);
GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read),
DoseImage.GetDevice(Intent.Write),
(uint)DoseImage.ElementsSliceComplex,
new[] { FrameDose },
NikoConst,
1);
PS.MultiplySlices(DoseImage);
//DoseImage.WriteMRC("dose.mrc");
DoseImage.Dispose();
}*/
#endregion
//Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
//PSAbs.Abs();
//FrameParticlesFT.Multiply(PS);
AverageFT.Add(FrameParticlesFT);
//Weights.Add(PSAbs);
//PS.Multiply(PS);
//AveragePS.Add(PS);
//PS.Dispose();
FrameParticlesFT.Dispose();
//PSAbs.Dispose();
}
FrameParticles.Dispose();
//CTFCoords.Dispose();
//AverageFT.Divide(Weights);
//AveragePS.Divide(Weights);
//AverageFT.Multiply(AveragePS);
Weights.Dispose();
Image AverageParticlesUncorrected = AverageFT.AsIFFT();
AverageFT.Dispose();
Image AverageParticles = AverageParticlesUncorrected.AsAnisotropyCorrected(new int2(DimsRegion),
(float)(CTF.PixelSize + CTF.PixelSizeDelta / 2M),
(float)(CTF.PixelSize - CTF.PixelSizeDelta / 2M),
(float)CTF.PixelSizeAngle * Helper.ToRad,
8);
AverageParticlesUncorrected.Dispose();
GPU.NormParticles(AverageParticles.GetDevice(Intent.Read),
AverageParticles.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / (PixelSize / 1.00f)),
true,
(uint)NParticles);
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader);
AverageParticles.Dispose();
//AveragePS.WriteMRC(ParticleCTFPath, ParticlesHeader);
AveragePS.Dispose();
float[] DistanceWeights = new float[NParticles];
for (int p1 = 0; p1 < NParticles - 1; p1++)
{
float2 Pos1 = new float2(Origins[p1].X, Origins[p1].Y);
for (int p2 = p1 + 1; p2 < NParticles; p2++)
{
float2 Pos2 = new float2(Origins[p2].X, Origins[p2].Y);
float2 Diff = Pos2 - Pos1;
float Dist = Diff.X * Diff.X + Diff.Y * Diff.Y;
Dist = 1f / Dist;
DistanceWeights[p1] += Dist;
DistanceWeights[p2] += Dist;
}
}
for (int i = 0; i < NParticles; i++)
{
string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
tableIn.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath);
//string ParticleCTFsPath = (i + 1).ToString("D6") + "@particlectf/" + RootName + "_particlectf.mrcs";
//tableIn.SetRowValue(RowIndices[i], "rlnCtfImage", ParticleCTFsPath);
tableIn.SetRowValue(RowIndices[i], "rlnAutopickFigureOfMerit", DistanceWeights[i].ToString(CultureInfo.InvariantCulture));
}
}
public void WriteMRC(string path, HeaderMRC header = null)
{
if (header == null)
header = new HeaderMRC();
header.Dimensions = IsFT ? DimsFT : Dims;
header.Dimensions.X *= IsComplex ? 2 : 1;
float[][] Data = GetHost(Intent.Read);
float Min = float.MaxValue, Max = -float.MaxValue;
Parallel.For(0, Data.Length, z =>
{
float LocalMin = MathHelper.Min(Data[z]);
float LocalMax = MathHelper.Max(Data[z]);
lock (Data)
{
Min = Math.Min(LocalMin, Min);
Max = Math.Max(LocalMax, Max);
}
});
header.MinValue = Min;
header.MaxValue = Max;
IOHelper.WriteMapFloat(path, header, GetHost(Intent.Read));
}